[phenixbb] Persistence of CONECT records?

Warren DeLano warren at delsci.com
Thu Apr 10 13:25:50 PDT 2008


Though I wouldn't mind PyMOL taking credit for CONECT valence encoding, this was in fact a convention originally employed by MacroModel which I adopted from Schrodinger.  
 
According to OpenBabel maintainer Geoff Hutchinson, it is also a convention supported by the OpenBabel chemical interchange software, and it according to OpenEye's docs, OEChem supports it as well (with the OEPDBFlag::ORDERS, BONDS, and BOTH flags to OEWritePDBFile).
 
Given that four popular tools already support this convention, shouldn't PHENIX do so as well?
 
________________________________


Message: 4
Date: Thu, 10 Apr 2008 12:53:27 -0400
From: "Schubert, Carsten [PRDUS]" <CSCHUBER at prdus.jnj.com>
Subject: [phenixbb] Persistence of CONNECT records?
To: <phenixbb at phenix-online.org>
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        <889E20E3723D0C45A493DA5DA87D854E01E876B6 at JNJUSRAGMS02.na.jnj.com>
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Hi,

I noticed that the CONNECT records of ligands generated in elbow get deleted in phenix.refine. Even specifing both the protein and ligand file (with CONNECT records) in the .def files, does not retain these records. For us they are coming in handy since they specify the bond order of the ligands. This is important for display in PyMol, which assigns bond orders based on these records.
Would it be possible to keep the CONNECT records in the output file of phenix.refine? Obviously the numbering would need to be adjusted and I have not yet checked if some of the model building programs like coot would be able to handle this situation correctly.


Cheers,

        Carsten


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Message: 5
Date: Thu, 10 Apr 2008 10:35:32 -0700
From: "Ralf W. Grosse-Kunstleve" <rwgk at cci.lbl.gov>
Subject: Re: [phenixbb] Ignoring SegIDs
To: phenixbb at phenix-online.org
Message-ID: <200804101735.m3AHZWsB017679 at cci.lbl.gov>
Content-Type: text/plain; charset=us-ascii

> There is potentially a worse problem from Coot (which I imagine Paul
> will fix sometime RSN) where you can end up with ChainID & SEGID
> different (from the Apply NCS loop command)

I hope my current algorithm handles this gracefully. But only when
it is out in the wild will we know for sure...
Ralf


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Message: 6
Date: Thu, 10 Apr 2008 10:48:15 -0700
From: "Ralf W. Grosse-Kunstleve" <rwgk at cci.lbl.gov>
Subject: Re: [phenixbb] Persistence of CONNECT records?
To: phenixbb at phenix-online.org
Message-ID: <200804101748.m3AHmFQc019690 at cci.lbl.gov>
Content-Type: text/plain; charset=us-ascii

> I noticed that the CONNECT records of ligands generated in elbow
> get deleted in phenix.refine. Even specifing both the protein and
> ligand file (with CONNECT records) in the .def files, does not retain
> these records. For us they are coming in handy since they specify the
> bond order of the ligands. This is important for display in PyMol,
> which assigns bond orders based on these records.
>
> Would it be possible to keep the CONNECT records in the output file
> of phenix.refine? Obviously the numbering would need to be adjusted
> and I have not yet checked if some of the model building programs
> like coot would be able to handle this situation correctly.

Yes, that's exactly why maintaining the CONECT records is a real
project. As an aside, the PyMOL trick of repeating records to convey
the bond order isn't used anywhere else as far as I know (but I like
the idea).
I'm in the middle of re-doing the fundamentals of how phenix.refine
handles pdb files. Once that's settled we will review how much effort
it would take to maintain CONECT records.

Ralf





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